Last night when I tried to carb sync, however I could not connect the carb sync'er onto carbs as its vacuum ports were buried so deep inside the carbs. So I adjusted the carb without carb sync by adjusting the synchro knob on the carb until I didn't hear any pop noises out of thre carb and didn't smell any fuel out of exhaust pipe. Since then the bike runs so much quicker with almost instant throttle response. But could this make shift carb synching give my engine lean mixture that ould cause engine knock? I am curious because current running condition seems to be too good for carb synching without the sync'er.

One cylinder could be working harder than the other, carrying the other one, and still make the engine sound smooth.

Eyeball synch it.
It can cause it to vibrate a lot especially at low rpm/throttle opening.
Cool.
Buddha.

Scratch: if one cylinder could be working harder than the other... a bad thing for crankshaft? As bad as running on one cylinder?
Buddha: I don't sense any vibration whatsoever. Rather it has less vibration than before. How do I eyeball synch?

Take off the crabs and look at the light, adjust synch screw till you see equal light in both butterflies. You can turn the idle screw down and down till its both equal at the smallest opening of the butterflies.
Cool.
Buddha.

It is as bad as running on one cylinder.

Do as Buddha has suggested, take the carbs off and point them at a light, so you can see light underneath each butterfly valve.  This will give you the best starting point towards synchronizing your carburetors.